> -----Ursprüngliche Nachricht----- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] Im Auftrag von Chandan Choudhury > Gesendet: Donnerstag, 29. November 2012 15:31 > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] g_tune_pme for multiple nodes > > Hi Carsten, > > Thanks for your suggestion. > > I did try to pass to total number of cores with the np flag to the g_tune_pme, > but it didnot help. Hopefully I am doing something silliy. I have pasted the > snippet of the PBS script. > > #!/bin/csh > #PBS -l nodes=2:ppn=12:twelve > #PBS -N bilayer_tune > .... > .... > .... > > cd $PBS_O_WORKDIR > export > MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" > mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x > tune.xtc -e tune.edr -g tune.log -nice 0
Hi, Don't start an MPI process. Run: g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x and everything should work fine. /Flo > > > Then I submit the script using qsub. > When I login to the compute nodes there I donot find and mdrun executable > running. > > I also tried using nodes=1 and np 12. It didnot work through qsub. > > Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 - > s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 > > It worked. > > Also, if I just use > $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g > tune.log -nice 0 g_tune_pme executes on the head node and writes various files. > > Kindly let me know what am I missing when I submit through qsub. > > Thanks > > Chandan > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner <ckut...@gwdg.de> wrote: > > > Hi Chandan, > > > > g_tune_pme also finds the optimal number of PME cores if the cores are > > distributed on multiple nodes. Simply pass the total number of cores > > to the -np option. Depending on the MPI and queue environment that you > > use, the distribution of the cores over the nodes may have to be > > specified in a hostfile / machinefile. Check g_tune_pme -h on how to > > set that. > > > > Best, > > Carsten > > > > > > On Aug 28, 2012, at 8:33 PM, Chandan Choudhury <iitd...@gmail.com> > wrote: > > > > > Dear gmx users, > > > > > > I am using 4.5.5 of gromacs. > > > > > > I was trying to use g_tune_pme for a simulation. I intend to execute > > > mdrun at multiple nodes with 12 cores each. Therefore, I would like > > > to optimize the number of pme nodes. I could execute g_tune_pme -np > > > 12 md.tpr. But this will only find the optimal PME nodes for single > > > nodes run. How do I find the optimal PME nodes for multiple nodes. > > > > > > Any suggestion would be helpful. > > > > > > Chandan > > > > > > -- > > > Chandan kumar Choudhury > > > NCL, Pune > > > INDIA > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > * Please don't post (un)subscribe requests to the list. Use the www > > > interface or send it to gmx-users-requ...@gromacs.org. > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > > Dr. Carsten Kutzner > > Max Planck Institute for Biophysical Chemistry Theoretical and > > Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany > > Tel. +49-551-2012313, Fax: +49-551-2012302 > > http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface or > send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists